The host controller will reset and re-enumerate a device after multiple failures at the transaction level, for example, if an endpoint doesn't respond to a token packet with ACK, NAK, etc.
The host controller knows nothing about handles or other application-level protocols.
The reset is the host's attempt to fix the problem.
The true solution is to find out why the errors are happening and fix it. The TotalPhase analyzer should show the error that is causing the reset.
If the host application attempts a transfer and discovers that the handle is closed, the application can attempt to obtain a new handle for the device.